Currently, for Serato DJ, the best way to do this is to use Serato Video (you don't need the full version, just the demo) to associate your files while offline. These associations will then be saved and can be used with MixEmergency as well. There is a system with MixEmergency to do this, but it needs to be updated for use with the later versions of Serato DJ (it was initially designed to work with Scratch Live). This is on my list of things to do, but I've had other tasks that have taken priority so far. As for choosing the start point of any video track, this isn't possible within MixEmergency at the moment - it will always sync to the start position of the audio and video.
